The last option would be the most radical and that would be to
disable the thread
sorting (and reverting to subject sorting) if not using a trash
mailbox and hiding
deleted messages.

What if we changed thread sorting to be more "conversations"-like, and
only showed the top-level message in the thread in the mailbox list?
Then show the whole thread in the message view if using thread
sorting. Would that make it easier? We could then consider a
"conversation" deleted only if all of the messages in it were deleted.